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abundancestats

Java code for various ecological abundance statistics

alignmenttools

Tools for pairwise sequence comparison, distance calculation, and hidden markov model sequence scoring (using HMMER3 models). Many RDP Projects require this package.

classifier

RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s

clustering

RDP memory-constrained hierarchical clustering tools.

ecofunprimer

primer design pipeline

framebot

Dynamic programming based frame shift detection and correction tool with nearest neighbor classification.

fungene_pipeline

Scripts and resources for analyzing sequence data for select eco-functional genes

fungeneutils

FungeneUtils package

gfclassify

Gene Family Classifier allows for fast and accurate classification of amplicon (or open reading frame) nucleotide sequences.

kb_rdptools

kbase app for rdp classifier

kmerfilter

Tools for kmer analysis.

probematch

Tools for finding (and removing) DNA/RNA primers in sequence reads.

rdptools

Collection of commonly used RDP Tools for easy building

readseq

Java based common sequence file format reader and sequence file manipulation. Most RDP projects require this package.

seqfilters

Java filtering framework for sequence data

sequencematch

K-mer based sequence matching tool

soap-examples

Code samples from various languages for interacting with RDP soap services

taxonomytree

TaxonomyTree building and traversal utility classes.

xander-hmmgs

xander_assembler

A gene-targeted assembler tool